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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ), 'gf_id' => 'HOM05D001172', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001172' ), 'data_identifier' => 'HOM05D001172', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001172', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02880' => 'bna', 'A01p07790' => 'bna', 'A03p63900' => 'bna', 'A05p28500' => 'bna', 'A06p33640' => 'bna', 'A06p34200' => 'bna', 'A07p03260' => 'bna', 'A07p40210' => 'bna', 'A08p19270' => 'bna', 'Aa31LG1G14550' => 'aar', 'Aa31LG4G4660' => 'aar', 'Aa31LG6G12790' => 'aar', 'Aa31LG8G15010' => 'aar', 'Aa31LG8G7210' => 'aar', 'Actinidia05095' => 'ach', 'Actinidia10735' => 'ach', 'Actinidia17408' => 'ach', 'Actinidia19024' => 'ach', 'Actinidia28731' => 'ach', 'Actinidia35009' => 'ach', 'Actinidia37947' => 'ach', 'Ah.02g113690' => 'amhyb', 'Ah.03g134310' => 'amhyb', 'Ah.09g234940' => 'amhyb', 'Ah.14g088030' => 'amhyb', 'AL2G34260' => 'aly', 'AL3G34110' => 'aly', 'AL3G50740' => 'aly', 'AL7G15230' => 'aly', 'AL8G45530' => 'aly', 'Aqoxy1G02163' => 'aox', 'Aqoxy3G03475' => 'aox', 'Aqoxy5G01109' => 'aox', 'Aqoxy6G02017' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SLH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1ZFB6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2P0YEY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37ETDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6C8X0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B7DDIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JM6ZP6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5VJ64' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0ZW9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VSS2FD' => 'arhy', 'AT1G74410' => 'ath', 'AT2G17730' => 'ath', 'AT3G20395' => 'ath', 'AT4G35840' => 'ath', 'AT5G66070' => 'ath', 'ATR0661G231' => 'atr', 'Atru.chr2.3410' => 'acertr', 'Atru.chr3.904' => 'acertr', 'Atru.chr9.214' => 'acertr', 'AUR62008443' => 'cqu', 'AUR62012703' => 'cqu', 'AUR62021647' => 'cqu', 'AUR62021956' => 'cqu', 'AUR62026228' => 'cqu', 'AUR62026410' => 'cqu', 'AUR62044528' => 'cqu', 'BcaB02g06943' => 'bca', 'BcaB03g16546' => 'bca', 'BcaB06g26105' => 'bca', 'BcaB06g28013' => 'bca', 'BcaB07g31733' => 'bca', 'BcaC01g01156' => 'bca', 'BcaC01g02890' => 'bca', 'BcaC01g02948' => 'bca', 'BcaC04g22949' => 'bca', 'BcaC04g23111' => 'bca', 'BcaC05g28325' => 'bca', 'BcaC06g36309' => 'bca', 'BcaC08g47001' => 'bca', 'BcaC09g51825' => 'bca', 'BcaNung00788' => 'bca', 'BcaNung02994' => 'bca', 'BcaNung04880' => 'bca', 'BcaNung05048' => 'bca', 'BolC1t00305H' => 'bol', 'BolC1t00852H' => 'bol', 'BolC3t18072H' => 'bol', 'BolC3t18073H' => 'bol', 'BolC3t18129H' => 'bol', 'BolC3t21185H' => 'bol', 'BolC6t39885H' => 'bol', 'BolC7t40954H' => 'bol', 'BolC7t46562H' => 'bol', 'BraA01t00269Z' => 'bra', 'BraA01t00723Z' => 'bra', 'BraA03t15459Z' => 'bra', 'BraA05t21728Z' => 'bra', 'BraA06t26299Z' => 'bra', 'BraA06t26352Z' => 'bra', 'BraA07t28126Z' => 'bra', 'BraA07t31566Z' => 'bra', 'BraA08t33888Z' => 'bra', 'BraA09t36661Z' => 'bra', 'C01p03200' => 'bna', 'C01p08680' => 'bna', 'C03p58000' => 'bna', 'C03p58700' => 'bna', 'C03p88740' => 'bna', 'C06p33370' => 'bna', 'C06p48560' => 'bna', 'C07p05550' => 'bna', 'C07p61360' => 'bna', 'CAN.G354.65' => 'can', 'CAN.G890.32' => 'can', 'CAN.G953.2' => 'can', 'CANSAT01G2753' => 'cansat', 'CARHR067670' => 'chi', 'CARHR096110' => 'chi', 'CARHR108050' => 'chi', 'CARHR238270' => 'chi', 'CARHR244210' => 'chi', 'CARHR281680' => 'chi', 'Carub.0002s2118' => 'cru', 'Carub.0003s2034' => 'cru', 'Carub.0003s3186' => 'cru', 'Carub.0007s0439' => 'cru', 'Carub.0008s2843' => 'cru', 'Ca_06321_v3' => 'car', 'Ca_14727_v3' => 'car', 'Ca_21810_v3' => 'car', 'Ca_24939_v3' => 'car', 'Ca_30810_v3' => 'car', 'CBR_g50130' => 'cbr', 'Cc00_g03100' => 'ccan', 'Cc04_g15150' => 'ccan', 'Cc05_g13670' => 'ccan', 'Cc07_g11290' => 'ccan', 'Cc11_g13970' => 'ccan', 'CDE05G0695' => 'cde', 'CDE07G1753' => 'cde', 'Cfa007027' => 'cfa', 'Cfa018917' => 'cfa', 'Ciclev10009352m.g' => 'ccl', 'Ciclev10009692m.g' => 'ccl', 'Ciclev10022213m.g' => 'ccl', 'Ciclev10026387m.g' => 'ccl', 'CiPaw.07G063100' => 'cil', 'CiPaw.08G126500' => 'cil', 'CiPaw.11G046900' => 'cil', 'CiPaw.11G189500' => 'cil', 'CiPaw.12G129900' => 'cil', 'ClCG10G000480' => 'cla', 'COL.COLO4_16052' => 'col', 'COL.COLO4_22492' => 'col', 'Cpa.g.sc111.27' => 'cpa', 'Cpa.g.sc12.307' => 'cpa', 'Cpa.g.sc26.270' => 'cpa', 'Cpa.g.sc6.310' => 'cpa', 'CsaV3_3G000540' => 'csa', 'CsaV3_7G021810' => 'csa', 'CSS0000285' => 'camsi', 'CSS0005429' => 'camsi', 'CSS0008804' => 'camsi', 'CSS0008926' => 'camsi', 'CSS0041529' => 'camsi', 'CSS0047768' => 'camsi', 'DCAR_011579' => 'dca', 'DCAR_016706' => 'dca', 'DCAR_031365' => 'dca', 'Dinv08550' => 'din', 'Dinv22261' => 'din', 'Dinv40755' => 'din', 'Duzib084G0738' => 'dzi', 'Duzib116G0510' => 'dzi', 'Duzib168G0733' => 'dzi', 'Duzib170G0724' => 'dzi', 'Duzib187G1536' => 'dzi', 'Duzib187G1869' => 'dzi', 'Duzib213G0183' => 'dzi', 'Duzib213G0996' => 'dzi', 'Duzib264G1174' => 'dzi', 'Duzib268G0132' => 'dzi', 'Duzib268G0571' => 'dzi', 'ECA232G3628' => 'eca', 'ECA233G1399' => 'eca', 'ECA236G3186' => 'eca', 'ECA240G2601' => 'eca', 'ECA246G1521' => 'eca', 'EL10Ac5g11051' => 'bvu', 'EL10Ac6g13331' => 'bvu', 'EL10Ac8g20051' => 'bvu', 'Eucgr.F00762' => 'egr', 'Eucgr.F03713' => 'egr', 'Eucgr.F03715' => 'egr', 'Eucgr.F03716' => 'egr', 'Eucgr.F03717' => 'egr', 'Eucgr.I02308' => 'egr', 'Eucgr.J02487' => 'egr', 'Eucgr.K02490' => 'egr', 'FAN08G1164' => 'fan', 'FAN11G1361' => 'fan', 'FAN16G0205' => 'fan', 'FAN18G3784' => 'fan', 'FAN19G2171' => 'fan', 'FAN23G2982' => 'fan', 'FAN26G0294' => 'fan', 'FAN28G2817' => 'fan', 'FvH4_1g11120' => 'fve', 'FvH4_3g22710' => 'fve', 'FvH4_5g14620' => 'fve', 'Glyma.01G162900' => 'gma', 'Glyma.02G044300' => 'gma', 'Glyma.02G291200' => 'gma', 'Glyma.04G143800' => 'gma', 'Glyma.05G025200' => 'gma', 'Glyma.08G316400' => 'gma', 'Glyma.11G080500' => 'gma', 'Glyma.16G121900' => 'gma', 'Glyma.17G101800' => 'gma', 'Glyma.18G096600' => 'gma', 'Gohir.A01G079600' => 'ghi', 'Gohir.A02G174100' => 'ghi', 'Gohir.A04G016700' => 'ghi', 'Gohir.A05G183550' => 'ghi', 'Gohir.A06G001200' => 'ghi', 'Gohir.A08G235200' => 'ghi', 'Gohir.A11G040900' => 'ghi', 'Gohir.A11G171900' => 'ghi', 'Gohir.A12G058800' => 'ghi', 'Gohir.A13G138000' => 'ghi', 'Gohir.D01G066801' => 'ghi', 'Gohir.D03G005700' => 'ghi', 'Gohir.D05G369500' => 'ghi', 'Gohir.D08G255600' => 'ghi', 'Gohir.D11G044200' => 'ghi', 'Gohir.D11G178800' => 'ghi', 'Gohir.D12G058800' => 'ghi', 'Gohir.D13G142800' => 'ghi', 'Gorai.002G088700' => 'gra', 'Gorai.003G006100' => 'gra', 'Gorai.004G272900' => 'gra', 'Gorai.007G047500' => 'gra', 'Gorai.007G190700' => 'gra', 'Gorai.008G062100' => 'gra', 'Gorai.009G191600' => 'gra', 'Gorai.009G438200' => 'gra', 'Gorai.010G001400' => 'gra', 'Gorai.013G159600' => 'gra', 'GSVIVG01005189001' => 'vvi', 'GSVIVG01007975001' => 'vvi', 'GSVIVG01037651001' => 'vvi', 'HanXRQChr03g0076511' => 'han', 'HanXRQChr09g0257201' => 'han', 'HanXRQChr11g0337691' => 'han', 'HanXRQChr12g0366751' => 'han', 'HanXRQChr13g0386721' => 'han', 'HanXRQChr13g0414531' => 'han', 'HanXRQChr14g0441671' => 'han', 'HanXRQChr14g0441991' => 'han', 'HanXRQChr15g0484751' => 'han', 'HanXRQChr15g0494371' => 'han', 'HanXRQChr16g0502821' => 'han', 'Haze_03706' => 'cav', 'Haze_07299' => 'cav', 'Haze_09677' => 'cav', 'Hma1.2p1_0060F.1_g033530' => 'hma', 'Hma1.2p1_0561F.1_g178980' => 'hma', 'HPP92_001750' => 'vpl', 'HPP92_001776' => 'vpl', 'HPP92_002366' => 'vpl', 'HPP92_014385' => 'vpl', 'HPP92_014395' => 'vpl', 'HPP92_021010' => 'vpl', 'HPP92_027593' => 'vpl', 'Hund02630' => 'sun', 'Hund14173' => 'sun', 'Hund16619' => 'sun', 'Hund21407' => 'sun', 'Hund23471' => 'sun', 'Lalb_Chr01g0006521' => 'lal', 'Lalb_Chr04g0248411' => 'lal', 'Lalb_Chr07g0178151' => 'lal', 'Lalb_Chr07g0180121' => 'lal', 'Lalb_Chr09g0321471' => 'lal', 'Lalb_Chr10g0106981' => 'lal', 'Lalb_Chr12g0196951' => 'lal', 'Lalb_Chr12g0199111' => 'lal', 'Lalb_Chr16g0377391' => 'lal', 'Lalb_Chr17g0348501' => 'lal', 'Lj2A484T46' => 'lonja', 'Lj2g0000668' => 'lja', 'Lj2g0002819' => 'lja', 'Lj4A225T62' => 'lonja', 'Lj4g0017899' => 'lja', 'Lj4g0023804' => 'lja', 'Lj4g0024604' => 'lja', 'LjContig00272g0027997' => 'lja', 'Lsat_1_v5_gn_2_75500' => 'lsa', 'Lsat_1_v5_gn_3_71041' => 'lsa', 'Lsat_1_v5_gn_4_108940' => 'lsa', 'Lsat_1_v5_gn_4_144221' => 'lsa', 'Lsat_1_v5_gn_7_108540' => 'lsa', 'Lsat_1_v5_gn_8_29380' => 'lsa', 'Lsat_1_v5_gn_9_93880' => 'lsa', 'Manes.01G150600' => 'mes', 'Manes.02G110100' => 'mes', 'Manes.03G129300' => 'mes', 'Manes.06G025800' => 'mes', 'Manes.14G081100' => 'mes', 'Manes.15G071700' => 'mes', 'Manes.18G009600' => 'mes', 'Mapoly0001s0307' => 'mpo', 'MBI02_g14232_MAGBIO' => 'mbi', 'MBI05_g16045_MAGBIO' => 'mbi', 'MBI09_g15821_MAGBIO' => 'mbi', 'MBI18_g14469_MAGBIO' => 'mbi', 'MD02G1123800' => 'mdo', 'MD03G1200700' => 'mdo', 'MD11G1217700' => 'mdo', 'MD14G1203800' => 'mdo', 'MD15G1237800' => 'mdo', 'Medtr4g108830' => 'mtr', 'Medtr4g108970' => 'mtr', 'Medtr5g022920' => 'mtr', 'Medtr5g092750' => 'mtr', 'Medtr5g092790' => 'mtr', 'Medtr8g074900' => 'mtr', 'MELO3C013744.2' => 'cme', 'MELO3C028997.2' => 'cme', 'Migut.H01826' => 'egut', 'Migut.L00905' => 'egut', 'Migut.M01766' => 'egut', 'MSTRG.12973' => 'ama', 'MSTRG.15148' => 'ama', 'MSTRG.15585' => 'ama', 'MSTRG.3613' => 'ama', 'MSTRG.6919' => 'ama', 'Nitab4.5_0000188g0240' => 'nta', 'Nitab4.5_0000981g0070' => 'nta', 'Nitab4.5_0001561g0100' => 'nta', 'Nitab4.5_0001685g0030' => 'nta', 'Nitab4.5_0002105g0040' => 'nta', 'Nitab4.5_0007385g0010' => 'nta', 'Nitab4.5_0008809g0040' => 'nta', 'Nitab4.5_0010106g0010' => 'nta', 'Nn1g00140' => 'nnu', 'Nn1g00142' => 'nnu', 'Nn3g17315' => 'nnu', 'Nn4g23261' => 'nnu', 'Nn5g29573' => 'nnu', 'Nn5g30840' => 'nnu', 'Nn6g31917' => 'nnu', 'Nn6g33558' => 'nnu', 'Nn6g33559' => 'nnu', 'Oeu005528.1' => 'oeu', 'Oeu007579.1' => 'oeu', 'Oeu013482.1' => 'oeu', 'Oeu020657.1' => 'oeu', 'Oeu031632.1' => 'oeu', 'Oeu037455.1' => 'oeu', 'Oeu042767.1' => 'oeu', 'Oeu042768.1' => 'oeu', 'Oeu042938.1' => 'oeu', 'Os02g0743700' => 'osa', 'Os06g0231600' => 'osa', 'Os06g0717600' => 'osa', 'Os07g0479100' => 'osa', 'Os08g0550400' => 'osa', 'Os09g0542600' => 'osa', 'Os10g0544600' => 'osa', 'Peaxi162Scf00153g01842' => 'pax', 'Peaxi162Scf00270g00077' => 'pax', 'Peaxi162Scf00328g00120' => 'pax', 'Peaxi162Scf00439g00037' => 'pax', 'Peaxi162Scf00718g00012' => 'pax', 'Peaxi162Scf01097g00415' => 'pax', 'PGR031G2124' => 'pgr', 'PGR083G1571' => 'pgr', 'PGR102G0738' => 'pgr', 'PGR102G2081' => 'pgr', 'PGR119G2262' => 'pgr', 'PGSC0003DMG400003661' => 'stu', 'PGSC0003DMG400022525' => 'stu', 'PGSC0003DMG400023881' => 'stu', 'PGSC0003DMG400027871' => 'stu', 'Phvul.002G105100' => 'pvu', 'Phvul.003G188700' => 'pvu', 'Phvul.003G267100' => 'pvu', 'Phvul.006G043600' => 'pvu', 'Phvul.008G266700' => 'pvu', 'Phvul.011G170800' => 'pvu', 'Potri.001G435800' => 'ptr', 'Potri.005G108200' => 'ptr', 'Potri.005G244800' => 'ptr', 'Potri.005G244900' => 'ptr', 'Potri.006G175700' => 'ptr', 'Potri.007G061400' => 'ptr', 'Potri.010G245801' => 'ptr', 'Potri.018G098000' => 'ptr', 'Potri.018G098100' => 'ptr', 'Prupe.4G182800' => 'ppe', 'Prupe.4G213600' => 'ppe', 'Prupe.5G197100' => 'ppe', 'Prupe.7G174700' => 'ppe', 'Psat2g010840' => 'psa', 'Psat2g011480' => 'psa', 'Psat2g152280' => 'psa', 'Psat4g049920' => 'psa', 'Psat4g102720' => 'psa', 'PSO017G5093' => 'pso', 'PSO170G6041' => 'pso', 'PSO210G6221' => 'pso', 'PSO478G3952' => 'pso', 'PSO541G3198' => 'pso', 'PSO541G4348' => 'pso', 'PSO675G0002' => 'pso', 'PSO675G1544' => 'pso', 'PSO832G2181' => 'pso', 'QL02p012721' => 'qlo', 'QL02p012783' => 'qlo', 'QL06p051995' => 'qlo', 'QL08p010134' => 'qlo', 'RcHm_v2.0_Chr2g0098401' => 'rch', 'RcHm_v2.0_Chr2g0132331' => 'rch', 'RcHm_v2.0_Chr4g0446061' => 'rch', 'RcHm_v2.0_Chr5g0035931' => 'rch', 'RcHm_v2.0_Chr5g0039601' => 'rch', 'RcHm_v2.0_Chr7g0181871' => 'rch', 'Rhsim06G0217200' => 'rsi', 'Rhsim07G0248800' => 'rsi', 'Rhsim07G0248900' => 'rsi', 'Rhsim07G0249000' => 'rsi', 'Rhsim07G0249100' => 'rsi', 'Rhsim08G0030300' => 'rsi', 'Rhsim10G0206300' => 'rsi', 'Rhsim12G0154500' => 'rsi', 'RhsimUnG0250400' => 'rsi', 'Sabra02G0013700' => 'sbr', 'Sabra05G0088600' => 'sbr', 'Sabra05G0189300' => 'sbr', 'Sabra06G0134400' => 'sbr', 'Sabra10G0191900' => 'sbr', 'Sabra11G0125700' => 'sbr', 'Sabra16G0289900' => 'sbr', 'Sabra18G0084700' => 'sbr', 'Sabra18G0084800' => 'sbr', 'Sc03g0003770' => 'sci', 'Sc05g0009200' => 'sci', 'Sc05g0009900' => 'sci', 'Sc12g0006480' => 'sci', 'Sed0002466' => 'sed', 'Sed0009030' => 'sed', 'Sed0027038' => 'sed', 'SEGI_04771' => 'sgi', 'SEGI_05553' => 'sgi', 'SGA_v2.0_scaffold172G38998' => 'sas', 'SGA_v2.0_scaffold229G43293' => 'sas', 'SGA_v2.0_scaffold45G17088' => 'sas', 'SMO146G0161' => 'smo', 'Solyc02g062040.3' => 'sly', 'Solyc02g083400.3' => 'sly', 'Solyc03g033330.3' => 'sly', 'Solyc12g005020.2' => 'sly', 'Sopen02g013000' => 'spe', 'Sopen02g028180' => 'spe', 'Sopen03g006110' => 'spe', 'Sopen12g001030' => 'spe', 'Sp2g30610' => 'spa', 'Sp3g18410' => 'spa', 'Sp3g31140' => 'spa', 'Sp5g29570' => 'spa', 'Sp7g28240' => 'spa', 'Sp7g33620' => 'spa', 'TAR374G1220' => 'tar', 'TAR376G0368' => 'tar', 'TAR381G0289' => 'tar', 'TAR381G1424' => 'tar', 'TAR626G0297' => 'tar', 'TAR628G0586' => 'tar', 'TAR629G0959' => 'tar', 'TAR636G2529' => 'tar', 'THA.LOC104803928' => 'tha', 'THA.LOC104807514' => 'tha', 'THA.LOC104812090' => 'tha', 'THA.LOC104816924' => 'tha', 'THA.LOC104819733' => 'tha', 'THA.LOC104826504' => 'tha', 'Thecc.01G011800' => 'tca', 'Thecc.03G093300' => 'tca', 'Thecc.07G036700' => 'tca', 'Thecc.09G162200' => 'tca', 'Thhalv10004883m.g' => 'esa', 'Thhalv10019108m.g' => 'esa', 'Thhalv10022113m.g' => 'esa', 'Thhalv10022835m.g' => 'esa', 'Thhalv10026127m.g' => 'esa', 'TPR.G1207' => 'tpr', 'TPR.G19512' => 'tpr', 'TPR.G25117' => 'tpr', 'TPR.G7673' => 'tpr', 'TPR.G9266' => 'tpr', 'TWI09G0532' => 'twi', 'TWI32G0455' => 'twi', 'TWI34G0281' => 'twi', 'TWI73G0608' => 'twi', 'unitig_32.g11837' => 'ugi', 'unitig_62.g23283' => 'ugi', 'unitig_747.g21810' => 'ugi', 'unitig_85.g27326' => 'ugi', 'vmacro11725' => 'vma', 'vmacro16526' => 'vma', 'vmacro16527' => 'vma', 'vmacro17153' => 'vma', 'vmacro18439' => 'vma', 'vmacro22206' => 'vma', 'VMungo0251G3326' => 'vmu', 'VMungo0540G1772' => 'vmu', 'VMungo0540G2111' => 'vmu', 'VMungo0647G1003' => 'vmu', 'VMungo1080G0315' => 'vmu', 'VMungo1215G1143' => 'vmu', 'VMungo1215G1764' => 'vmu', 'VMungo1215G3322' => 'vmu', 'Zm00001eb022630' => 'zma', 'Zm00001eb039970' => 'zma', 'Zm00001eb104970' => 'zma', 'Zm00001eb180470' => 'zma', 'Zm00001eb194620' => 'zma', 'Zm00001eb202890' => 'zma', 'Zm00001eb228180' => 'zma', 'Zm00001eb238430' => 'zma', 'Zm00001eb254430' => 'zma', 'Zm00001eb279770' => 'zma', 'Zm00001eb321320' => 'zma', 'Zm00001eb331730' => 'zma' ) $gf_id = 'HOM05D001172' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001172' ) $data_identifier = 'HOM05D001172' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 9, 'sbr' => (int) 9, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331730' $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